@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (940) hide show
  1. package/dist/2dmaf-VTMPVZGT.js +1367 -0
  2. package/dist/AggMatrixInput-CH3RQ2QC.js +406 -0
  3. package/dist/AggMatrixInput-CH3RQ2QC.js.map +7 -0
  4. package/dist/AggregateMatrix-DPCHUOMF.js +41 -0
  5. package/dist/AppHeader-RA7T467G.js +830 -0
  6. package/dist/BoxPlot-7Q7SMT26.js +1211 -0
  7. package/dist/CorrelationVolcano-YV4UHOAX.js +617 -0
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  9. package/dist/Cuminc-ZN53C3MD.js +1219 -0
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  15. package/dist/Disco-PTZQF7IM.js +3389 -0
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  23. package/dist/GeneExpInput-DYBK54HC.js +42 -0
  24. package/dist/Geomap-QRD2WZVL.js +84 -0
  25. package/dist/HicApp-VKET4QHD.js +2245 -0
  26. package/dist/IDCViewer-RLLTXGD7.js +10812 -0
  27. package/dist/NumBinaryEditor-GYHOYPQL.js +279 -0
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  43. package/dist/ProteomeInput-4N2G6IFX.js +388 -0
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  188. package/dist/dnaMethylation-CX22TSRO.js +33 -0
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  846. /package/dist/{matrix.groups-URBU775S.js.map → matrix.groups-F62TSKIG.js.map} +0 -0
  847. /package/dist/{matrix.interactivity-W5AFOAQN.js.map → matrix.interactivity-2FBXB52E.js.map} +0 -0
  848. /package/dist/{matrix.layout-LU3NIJAL.js.map → matrix.layout-6TPVKLSX.js.map} +0 -0
  849. /package/dist/{matrix.legend-LTP6ETZO.js.map → matrix.legend-L4ULBMGX.js.map} +0 -0
  850. /package/dist/{matrix.renderers-762XI65L.js.map → matrix.renderers-DK6YRLO2.js.map} +0 -0
  851. /package/dist/{matrix.serieses-FHDBRPZA.js.map → matrix.serieses-DCRJLJ3H.js.map} +0 -0
  852. /package/dist/{matrix.sort-Q6A6UWMY.js.map → matrix.sort-XSGPH44J.js.map} +0 -0
  853. /package/dist/{matrix.sort.unit.spec-CTCOPKVS.js.map → matrix.sort.unit.spec-JF75F4I4.js.map} +0 -0
  854. /package/dist/{matrix.sorterUi-4M5AU5EL.js.map → matrix.sorterUi-WL5I6S3K.js.map} +0 -0
  855. /package/dist/{matrix.sorterUi.unit.spec-Y7GC3PM5.js.map → matrix.sorterUi.unit.spec-66JMV5BK.js.map} +0 -0
  856. /package/dist/{matrix.unit.spec-DROPHFTM.js.map → matrix.unit.spec-36AR4I43.js.map} +0 -0
  857. /package/dist/{mavb-BWA73N3U.js.map → mavb-ZH4RO77H.js.map} +0 -0
  858. /package/dist/{mds.fimo-3UJWIH2J.js.map → mds.fimo-MVP2G5PS.js.map} +0 -0
  859. /package/dist/{mds.samplescatterplot-EUS7DCSQ.js.map → mds.samplescatterplot-GYJ3OI4N.js.map} +0 -0
  860. /package/dist/{mds.survivalplot-77UEBQIC.js.map → mds.survivalplot-Q6MYQGTB.js.map} +0 -0
  861. /package/dist/{multivalue-KZ2DMVIR.js.map → multivalue-BGFMPH4X.js.map} +0 -0
  862. /package/dist/{numericDictTermCluster-C2MYJYPZ.js.map → numericDictTermCluster-FNNVLIWB.js.map} +0 -0
  863. /package/dist/{oncomatrix-6LGB3M7R.js.map → oncomatrix-LIIALWWN.js.map} +0 -0
  864. /package/dist/{oncomatrix.spec-UWMSLOHW.js.map → oncomatrix.spec-NEMLM2ZN.js.map} +0 -0
  865. /package/dist/{plot.2dvaf-LZAVWH65.js.map → plot.2dvaf-HJO3SKNK.js.map} +0 -0
  866. /package/dist/{plot.app-OEWE3AYV.js.map → plot.app-WSLFOFSR.js.map} +0 -0
  867. /package/dist/{plot.barplot-VIBHGTUT.js.map → plot.barplot-SPI5JA37.js.map} +0 -0
  868. /package/dist/{plot.boxplot-NQI3PSKR.js.map → plot.boxplot-4W3XEY5I.js.map} +0 -0
  869. /package/dist/{plot.brainImaging-3MTTCZHI.js.map → plot.brainImaging-KEOUTYIB.js.map} +0 -0
  870. /package/dist/{plot.disco-HODBY7SO.js.map → plot.disco-7IDMKNAQ.js.map} +0 -0
  871. /package/dist/{plot.ssgq-4URQE673.js.map → plot.ssgq-IOKUGDC4.js.map} +0 -0
  872. /package/dist/{plot.vaf2cov-QIJNEKCK.js.map → plot.vaf2cov-SFSZ6M43.js.map} +0 -0
  873. /package/dist/{polar2-GVFQNSLK.js.map → polar2-PLPE5TX5.js.map} +0 -0
  874. /package/dist/{profileForms-Z22CJXI4.js.map → profileForms-ZDHG67GM.js.map} +0 -0
  875. /package/dist/{profilePlot-IVQZBSID.js.map → profilePlot-UUZA2YG6.js.map} +0 -0
  876. /package/dist/{proteinView-AUK634AU.js.map → proteinView-GHS3XARL.js.map} +0 -0
  877. /package/dist/{proteomeCohortCompare-7G2F35H5.js.map → proteomeCohortCompare-TQ3BGIPS.js.map} +0 -0
  878. /package/dist/{pseudobulk-QTCUSH5I.js.map → pseudobulk-ODXYIUD5.js.map} +0 -0
  879. /package/dist/{qualitative-7ST7SSBT.js.map → qualitative-WOSYAIGQ.js.map} +0 -0
  880. /package/dist/{radar2-CEE6SNBS.js.map → radar2-2KXBS3Y3.js.map} +0 -0
  881. /package/dist/{radarFacility2-OSKDYIK7.js.map → radarFacility2-JCOKJQQF.js.map} +0 -0
  882. /package/dist/{rememberedGvQ.unit.spec-RYFUJ2NW.js.map → rememberedGvQ.unit.spec-DYRO2LO5.js.map} +0 -0
  883. /package/dist/{render-MAD3WMVD.js.map → render-IJ6GE3NE.js.map} +0 -0
  884. /package/dist/{report-6JXJVSEB.js.map → report-WLLFUA7L.js.map} +0 -0
  885. /package/dist/{sampleView-SG3QYZKQ.js.map → sampleView-LPKSYUNF.js.map} +0 -0
  886. /package/dist/{samplelst-R765UFP6.js.map → samplelst-MNI2MGMT.js.map} +0 -0
  887. /package/dist/{samplematrix-EBJYE5SM.js.map → samplematrix-KEKJP2B4.js.map} +0 -0
  888. /package/dist/{sc-7ZXPFDHD.js.map → sc-ZYKFRJU4.js.map} +0 -0
  889. /package/dist/{scatter-3GUL4KF3.js.map → scatter-BAEZOFWA.js.map} +0 -0
  890. /package/dist/{selectGenomeWithTklst-K4YXGJYG.js.map → selectGenomeWithTklst-HBHRXEDY.js.map} +0 -0
  891. /package/dist/{singleCellCellType-TU5VTPLP.js.map → singleCellCellType-PMFDV24B.js.map} +0 -0
  892. /package/dist/{singleCellCellType.unit.spec-IRITQIGT.js.map → singleCellCellType.unit.spec-ZLYDUDIY.js.map} +0 -0
  893. /package/dist/{singleCellGeneExpression-3IL52QDK.js.map → singleCellGeneExpression-SUYO3HR3.js.map} +0 -0
  894. /package/dist/{singleCellGeneExpression.unit.spec-WXC4C37T.js.map → singleCellGeneExpression.unit.spec-3N3HRXFN.js.map} +0 -0
  895. /package/dist/{singleCellPlot-XG3HZS7I.js.map → singleCellNumericValue-BV7C6Y34.js.map} +0 -0
  896. /package/dist/{snp-RMZRB426.js.map → singleCellPlot-BG7UJOHA.js.map} +0 -0
  897. /package/dist/{singlecell-BRF2HAV2.js.map → singlecell-BANNFGBS.js.map} +0 -0
  898. /package/dist/{singlecell-KVCJF2HI.js.map → singlecell-ZUTL5ZWE.js.map} +0 -0
  899. /package/dist/{ssGSEA-7RKWYZKX.js.map → snp-BHG4NVK4.js.map} +0 -0
  900. /package/dist/{snp.unit.spec-JF6KR2NT.js.map → snp.unit.spec-Q3AZHQRC.js.map} +0 -0
  901. /package/dist/{snplocus-AHUFHQ3Q.js.map → snplocus-HTJL63M3.js.map} +0 -0
  902. /package/dist/{spliceevent.a53ss.diagram-OSZZ2CF2.js.map → spliceevent.a53ss.diagram-UKRIP7EP.js.map} +0 -0
  903. /package/dist/{spliceevent.exonskip.diagram-AMA2D2OL.js.map → spliceevent.exonskip.diagram-CU777CXQ.js.map} +0 -0
  904. /package/dist/{spliceevent.noeventdiagram-RKTUXH5D.js.map → spliceevent.noeventdiagram-LGLXCF25.js.map} +0 -0
  905. /package/dist/{summarizeMutationDiagnosis-GCL4SRON.js.map → ssGSEA-BIEEKAKX.js.map} +0 -0
  906. /package/dist/{ssGSEA.unit.spec-XLCZHH7S.js.map → ssGSEA.unit.spec-YD4UDIRH.js.map} +0 -0
  907. /package/dist/{stattable-NDYUCLVZ.js.map → stattable-LFR3RSD6.js.map} +0 -0
  908. /package/dist/{studyCatalog-TAXRF5NS.js.map → studyCatalog-RINIZ277.js.map} +0 -0
  909. /package/dist/{summarizeCnvGeneexp-3QLHU6N7.js.map → summarizeCnvGeneexp-ZQFNPR65.js.map} +0 -0
  910. /package/dist/{summarizeGeneexpSurvival-ARI4MPFX.js.map → summarizeGeneexpSurvival-GIS7XMMH.js.map} +0 -0
  911. /package/dist/{summarizeMutationCnv-W7V7CKPI.js.map → summarizeMutationCnv-FWF7YIGR.js.map} +0 -0
  912. /package/dist/{summary-OUYDWLBF.js.map → summarizeMutationDiagnosis-V5L2OKTK.js.map} +0 -0
  913. /package/dist/{summarizeMutationSurvival-6TTMSRRX.js.map → summarizeMutationSurvival-LAUUF6XN.js.map} +0 -0
  914. /package/dist/{termCollection-7P3WU6X6.js.map → summary-OMU3ACNE.js.map} +0 -0
  915. /package/dist/{summary.integration.spec-4GTCG6HY.js.map → summary.integration.spec-6JZAT73L.js.map} +0 -0
  916. /package/dist/{summaryInput-UK3TLC7M.js.map → summaryInput-QIKL3HDD.js.map} +0 -0
  917. /package/dist/{sunburst-2UFHMNH3.js.map → sunburst-32IW2R57.js.map} +0 -0
  918. /package/dist/{survival-SPWYSDVB.js.map → survival-BMOPVAN2.js.map} +0 -0
  919. /package/dist/{survival-TL6UZ6FQ.js.map → survival-H5AWMQ36.js.map} +0 -0
  920. /package/dist/{svgraph-Z543MLIN.js.map → svgraph-B75FS3BB.js.map} +0 -0
  921. /package/dist/{svmr-SZCAOAIF.js.map → svmr-IUEUOHVO.js.map} +0 -0
  922. /package/dist/{table-IAQ6J4DO.js.map → table-YAAH7WR6.js.map} +0 -0
  923. /package/dist/{termCollection-3NGHR7QN.js.map → termCollection-7F5ZG2DB.js.map} +0 -0
  924. /package/dist/{termCollectionFractionSelection-YKIE6BME.js.map → termCollection-KNFUELYY.js.map} +0 -0
  925. /package/dist/{termCollection.unit.spec-EPYC7LOA.js.map → termCollection.unit.spec-S6M6QC4C.js.map} +0 -0
  926. /package/dist/{tk-X454XH5N.js.map → termCollectionFractionSelection-X22VMJWY.js.map} +0 -0
  927. /package/dist/{termCollectionFractionSelection.unit.spec-AG2CZPGZ.js.map → termCollectionFractionSelection.unit.spec-ELU6SD7P.js.map} +0 -0
  928. /package/dist/{tvs.dt-U77PCG6X.js.map → tk-TT666UVE.js.map} +0 -0
  929. /package/dist/{tk-TOXMU4GT.js.map → tk-UOPNJ323.js.map} +0 -0
  930. /package/dist/{tp.ui-FDQ76KPL.js.map → tp.ui-HGAHRKO5.js.map} +0 -0
  931. /package/dist/{vocabulary-64GO4YDB.js.map → tvs.dt-H7YYR4EB.js.map} +0 -0
  932. /package/dist/{tvs.dtcnv.categorical-XYZU4XLO.js.map → tvs.dtcnv.categorical-IPJTKGMF.js.map} +0 -0
  933. /package/dist/{tvs.dtcnv.continuous-4GJILFGP.js.map → tvs.dtcnv.continuous-XY5XZ4GH.js.map} +0 -0
  934. /package/dist/{tvs.dtfusion-7YROAHVI.js.map → tvs.dtfusion-VFCBMXRM.js.map} +0 -0
  935. /package/dist/{tvs.dtitd-MIYU4ZHH.js.map → tvs.dtitd-RZVW6FTR.js.map} +0 -0
  936. /package/dist/{tvs.dtsnvindel-XLDY7KWB.js.map → tvs.dtsnvindel-IDPJWSGC.js.map} +0 -0
  937. /package/dist/{tvs.dtsv-YMLJ37YR.js.map → tvs.dtsv-QERP756F.js.map} +0 -0
  938. /package/dist/{tvs.samplelst-KIVEXJKD.js.map → tvs.samplelst-6KNDHBIU.js.map} +0 -0
  939. /package/dist/{tvs.termCollection-4CQV3EB3.js.map → tvs.termCollection-GWPJK3NE.js.map} +0 -0
  940. /package/dist/{wsi.direct-5MQVRJZX.js.map → wsi.direct-2RBCBXDA.js.map} +0 -0
@@ -1,477 +0,0 @@
1
- import {
2
- axisstyle,
3
- sayerror,
4
- to_svg
5
- } from "./chunk-PC4MFDHP.js";
6
- import "./chunk-HJ6L54YS.js";
7
- import "./chunk-KV4W2ACA.js";
8
- import "./chunk-HPAW7XDM.js";
9
- import {
10
- Menu
11
- } from "./chunk-ELJX3QIQ.js";
12
- import "./chunk-BZN2O76M.js";
13
- import "./chunk-EEB5VE2A.js";
14
- import "./chunk-6RRZRISL.js";
15
- import "./chunk-2KM4PRQM.js";
16
- import {
17
- dofetch
18
- } from "./chunk-52QHIKH2.js";
19
- import "./chunk-A2ORIMUJ.js";
20
- import "./chunk-PPSWNLMG.js";
21
- import {
22
- bplen
23
- } from "./chunk-RUBZCKIX.js";
24
- import "./chunk-WINIL2KN.js";
25
- import "./chunk-PF4DSFDR.js";
26
- import "./chunk-7X6NF7NI.js";
27
- import "./chunk-W5J3LTYS.js";
28
- import {
29
- axisBottom,
30
- axisLeft,
31
- category10_default
32
- } from "./chunk-Z2ZITHT4.js";
33
- import {
34
- linear,
35
- ordinal
36
- } from "./chunk-4OLM3KSB.js";
37
- import "./chunk-FXQXCOII.js";
38
- import "./chunk-TLT4YIG3.js";
39
- import "./chunk-5R63Q5KH.js";
40
- import {
41
- select_default
42
- } from "./chunk-I6Y4O3RR.js";
43
- import "./chunk-Q5RDQNIT.js";
44
- import "./chunk-DQC5FFGV.js";
45
- import "./chunk-HS5PO5ZQ.js";
46
-
47
- // src/mds.survivalplot.js
48
- async function init(obj, holder, debugmode) {
49
- if (debugmode) {
50
- window.obj = obj;
51
- }
52
- obj.plots = [];
53
- obj.menu = new Menu({ padding: "5px" });
54
- obj.tip = new Menu({ padding: "5px" });
55
- obj.errordiv = holder.append("div").style("margin", "10px");
56
- obj.sayerror = (e) => {
57
- sayerror(obj.errordiv, typeof e == "string" ? e : e.message);
58
- if (e.stack) console.log(e.stack);
59
- };
60
- obj.uidiv = holder.append("div").style("margin", "20px");
61
- obj.plotdiv = holder.append("div").style("margin", "20px");
62
- obj.legendtable = holder.append("table").style("border-spacing", "5px");
63
- holder.append("button").text("SVG").on("click", () => {
64
- to_svg(obj.plotlist[0].svg.node(), "Survival");
65
- });
66
- try {
67
- await init_dataset_config(obj);
68
- if (!obj.plotlist) {
69
- obj.plotlist = [];
70
- }
71
- if (!Array.isArray(obj.plotlist)) throw ".plotlist should be array";
72
- if (obj.plotlist.length == 0) {
73
- const p = {
74
- type: obj.plottypes[0].key
75
- };
76
- obj.plotlist.push(p);
77
- }
78
- for (const p of obj.plotlist) {
79
- init_a_plot(p, obj);
80
- }
81
- } catch (e) {
82
- if (e.stack) console.log(e.stack);
83
- obj.sayerror("Cannot make plot: " + (e.message || e));
84
- }
85
- }
86
- function init_dataset_config(obj) {
87
- const par = {
88
- genome: obj.genome.name,
89
- dslabel: obj.mds.label,
90
- init: 1
91
- };
92
- return dofetch("mdssurvivalplot", par).then((data) => {
93
- if (data.error) throw data.error;
94
- if (!data.plottypes) throw "plottypes[] missing";
95
- obj.plottypes = data.plottypes;
96
- obj.samplegroupings = data.samplegroupings;
97
- });
98
- }
99
- function init_a_plot(p, obj) {
100
- init_a_plot_filldefault(p, obj);
101
- const div = obj.uidiv.append("div").style("margin", "20px");
102
- if (obj.plottypes.length > 1) {
103
- const s = div.append("div").style("margin-bottom", "10px").append("select").on("change", (event) => {
104
- p.type = event.target.options[event.target.selectedIndex].value;
105
- });
106
- for (const [i, t] of obj.plottypes.entries()) {
107
- s.append("option").text(t.name).property("value", t.key);
108
- if (t.key == p.type) {
109
- s.node().selectedIndex = i;
110
- }
111
- }
112
- }
113
- if (obj.samplegroupings && !p.samplerule.full.immutable) {
114
- const row = div.append("div").style("margin-bottom", "20px");
115
- const custom_input_row = div.append("div").style("display", "none");
116
- row.append("span").html("Choose samples from ").style("opacity", 0.5);
117
- const attr2select = {};
118
- const s = row.append("select").style("margin-right", "5px").on("change", (event) => {
119
- for (const k in attr2select) {
120
- attr2select[k].style("display", "none");
121
- }
122
- const o = event.target.options[event.target.selectedIndex];
123
- custom_input_row.style("display", o.usesampleset ? "block" : "none");
124
- if (o.useall) {
125
- p.samplerule.full.useall = 1;
126
- delete p.samplerule.full.byattr;
127
- return;
128
- }
129
- if (o.usesampleset) {
130
- delete p.samplerule.full.byattr;
131
- delete p.samplerule.full.useall;
132
- p.samplerule.full.usesampleset = 1;
133
- show_sampleinput(p, custom_input_row);
134
- return;
135
- }
136
- delete p.samplerule.full.useall;
137
- p.samplerule.full.byattr = 1;
138
- p.samplerule.key = o.key;
139
- const s3 = attr2select[o.key];
140
- s3.style("display", "inline");
141
- p.samplerule.full.value = s3.node().options[s3.node().selectedIndex].value;
142
- });
143
- for (const [i, attr] of obj.samplegroupings.entries()) {
144
- s.append("option").text(attr.label).property("key", attr.key);
145
- const usingthisattr = p.samplerule.full.byattr && p.samplerule.full.key == attr.key;
146
- if (usingthisattr) {
147
- s.node().selectedIndex = i;
148
- }
149
- const s2 = row.append("select").on("change", (event) => {
150
- p.samplerule.full.value = event.target.options[event.target.selectedIndex].value;
151
- });
152
- attr2select[attr.key] = s2;
153
- s2.style("display", usingthisattr ? "inline" : "none");
154
- for (const [j, v] of attr.values.entries()) {
155
- s2.append("option").text(v.value + " (n=" + v.count + ")").property("value", v.value);
156
- if (usingthisattr && v.value == p.samplerule.full.value) {
157
- s2.node().selectedIndex = j;
158
- }
159
- }
160
- }
161
- s.append("option").text("all samples").property("useall", 1);
162
- if (p.samplerule.full.useall) {
163
- s.node().selectedIndex = obj.samplegroupings.length;
164
- }
165
- s.append("option").text("custom sampleset").property("usesampleset", 1);
166
- }
167
- show_dividerules(p, div);
168
- p.button = div.append("button").text("Make plot").on("click", () => {
169
- loadPlot(p, obj);
170
- });
171
- p.d = obj.plotdiv.append("div").style("margin", "20px"), p.legend = {
172
- d_pvalue: p.d.append("div").style("margin", "10px"),
173
- d_samplefull: p.d.append("div").style("margin", "10px"),
174
- d_curves: p.d.append("div").style("margin", "10px")
175
- };
176
- p.svg = p.d.append("svg");
177
- p.resize_handle = p.d.append("div").append("div").attr("class", "sja_clbtext").text("drag to resize").style("float", "right");
178
- if (p.renderplot) {
179
- loadPlot(p, obj);
180
- }
181
- }
182
- function init_a_plot_filldefault(p, obj) {
183
- if (!p.type) {
184
- p.type = obj.plottypes[0].key;
185
- }
186
- if (!p.samplerule) {
187
- p.samplerule = {};
188
- }
189
- if (!p.samplerule.full) {
190
- p.samplerule.full = {};
191
- }
192
- if (obj.samplegroupings) {
193
- if (!p.samplerule.full.useall) {
194
- p.samplerule.full.byattr = 1;
195
- if (!p.samplerule.full.key) {
196
- p.samplerule.full.key = obj.samplegroupings[0].key;
197
- p.samplerule.full.value = obj.samplegroupings[0].values[0].value;
198
- }
199
- }
200
- } else {
201
- p.samplerule.full.useall = 1;
202
- }
203
- if (p.samplerule.set) {
204
- const st = p.samplerule.set;
205
- if (st.geneexpression) {
206
- if (!st.bymedian && !st.byquartile) {
207
- st.bymedian = 1;
208
- }
209
- }
210
- }
211
- if (!p.width) p.width = 500;
212
- if (!p.height) p.height = 500;
213
- if (!p.toppad) p.toppad = 10;
214
- if (!p.rightpad) p.rightpad = 10;
215
- if (!p.xaxispad) p.xaxispad = 10;
216
- if (!p.yaxispad) p.yaxispad = 10;
217
- if (!p.xaxish) p.xaxish = 40;
218
- if (!p.yaxisw) p.yaxisw = 65;
219
- if (!p.censorticksize) p.censorticksize = 6;
220
- if (!p.tickfontsize) p.tickfontsize = 14;
221
- if (!p.labfontsize) p.labfontsize = 15;
222
- }
223
- function doPlot(plot, obj) {
224
- const colorfunc = ordinal(category10_default);
225
- const minx = 0;
226
- let maxx = 0;
227
- for (const curve of plot.samplesets) {
228
- curve.color = colorfunc(curve.name);
229
- for (const s of curve.steps) {
230
- maxx = Math.max(maxx, s.x);
231
- }
232
- }
233
- plot.svg.selectAll("*").remove();
234
- const curves_g = plot.svg.append("g");
235
- for (const curve of plot.samplesets) {
236
- curve.path = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
237
- curve.ticks = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
238
- }
239
- const yaxis_g = plot.svg.append("g");
240
- const yaxis_scale = linear().domain([0, 1]);
241
- const yaxis_lab_g = plot.svg.append("g");
242
- const yaxis_lab = yaxis_lab_g.append("text").text("Survival").attr("transform", "rotate(-90)");
243
- const xaxis_g = plot.svg.append("g");
244
- const xaxis_scale = linear().domain([minx, maxx]);
245
- const xaxis_lab = plot.svg.append("text").attr("font-size", plot.labfontsize).text(obj.plottypes.find((i) => i.key == plot.type).timelabel).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
246
- function resize() {
247
- curves_g.attr("transform", "translate(" + (plot.yaxisw + plot.yaxispad) + "," + plot.toppad + ")");
248
- for (const curve of plot.samplesets) {
249
- const ticks = [];
250
- const pathd = ["M 0 0"];
251
- for (const s of curve.steps) {
252
- pathd.push("H " + plot.width * s.x / maxx);
253
- const y = plot.height * (s.y + s.drop);
254
- pathd.push("V " + y);
255
- if (s.censored) {
256
- const y2 = plot.height * s.y;
257
- for (const c of s.censored) {
258
- const x = plot.width * c / maxx;
259
- ticks.push(
260
- "M " + (x - plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l " + plot.censorticksize + " " + plot.censorticksize + " M " + (x + plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l -" + plot.censorticksize + " " + plot.censorticksize
261
- );
262
- }
263
- }
264
- }
265
- curve.path.attr("d", pathd.join(" "));
266
- if (ticks.length) {
267
- curve.ticks.attr("d", ticks.join(" "));
268
- }
269
- }
270
- yaxis_g.attr("transform", "translate(" + plot.yaxisw + "," + plot.toppad + ")");
271
- axisstyle({
272
- axis: yaxis_g.call(
273
- axisLeft().scale(yaxis_scale.range([plot.height, 0])).ticks(Math.floor(plot.height / (plot.tickfontsize + 20)))
274
- ),
275
- showline: 1,
276
- fontsize: plot.tickfontsize
277
- });
278
- yaxis_lab_g.attr("transform", "translate(" + plot.labfontsize + "," + (plot.toppad + plot.height / 2) + ")");
279
- yaxis_lab.attr("font-size", plot.labfontsize);
280
- xaxis_g.attr(
281
- "transform",
282
- "translate(" + (plot.yaxisw + plot.yaxispad) + "," + (plot.toppad + plot.height + plot.xaxispad) + ")"
283
- );
284
- let xticknumber;
285
- xaxis_g.append("text").text(maxx).attr("font-size", plot.tickfontsize).each(function() {
286
- xticknumber = Math.floor(plot.width / (this.getBBox().width + 30));
287
- }).remove();
288
- axisstyle({
289
- axis: xaxis_g.call(
290
- axisBottom().scale(xaxis_scale.range([0, plot.width])).ticks(xticknumber)
291
- ),
292
- showline: 1,
293
- fontsize: plot.tickfontsize
294
- });
295
- xaxis_lab.attr("font-size", plot.labfontsize).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
296
- plot.svg.attr("width", plot.yaxisw + plot.yaxispad + plot.width + plot.rightpad).attr("height", plot.toppad + plot.height + plot.xaxispad + plot.xaxish);
297
- }
298
- resize();
299
- plot.resize_handle.on("mousedown", (event) => {
300
- event.preventDefault();
301
- const b = select_default(document.body);
302
- const x = event.clientX;
303
- const y = event.clientY;
304
- const w0 = plot.width;
305
- const h0 = plot.height;
306
- b.on("mousemove", () => {
307
- plot.width = w0 + event.clientX - x;
308
- plot.height = h0 + event.clientY - y;
309
- resize();
310
- });
311
- b.on("mouseup", () => {
312
- b.on("mousemove", null).on("mouseup", null);
313
- });
314
- });
315
- if (Number.isFinite(plot.pvalue)) {
316
- plot.legend.d_pvalue.style("display", "block").text("P-value: " + plot.pvalue);
317
- } else {
318
- plot.legend.d_pvalue.style("display", "none");
319
- }
320
- plot.legend.d_curves.selectAll("*").remove();
321
- for (const c of plot.samplesets) {
322
- plot.legend.d_curves.append("div").style("margin", "3px").html(
323
- '<span style="background:' + c.color + '">&nbsp;&nbsp;</span> ' + c.name + (c.pvalue == void 0 ? "" : ", P-value: " + c.pvalue)
324
- );
325
- }
326
- }
327
- function loadPlot(plot, obj) {
328
- plot.button.text("Loading...").attr("disabled", 1);
329
- const par = {
330
- genome: obj.genome.name,
331
- dslabel: obj.mds.label,
332
- type: plot.type,
333
- samplerule: plot.samplerule
334
- };
335
- dofetch("mdssurvivalplot", par).then((data) => {
336
- if (data.error) throw data.error;
337
- if (!data.samplesets) throw "samplesets[] missing";
338
- plot.samplesets = data.samplesets;
339
- plot.pvalue = data.pvalue;
340
- doPlot(plot, obj);
341
- if (plot.samplerule.set && plot.samplerule.set.mutation) {
342
- if (plot.mutation_count.cnv) plot.mutation_count.cnv.html("(n=" + data.count_cnv + ")&nbsp;");
343
- if (plot.mutation_count.loh) plot.mutation_count.loh.html("(n=" + data.count_loh + ")&nbsp;");
344
- if (plot.mutation_count.snvindel) plot.mutation_count.snvindel.html("(n=" + data.count_snvindel + ")&nbsp;");
345
- if (plot.mutation_count.sv) plot.mutation_count.sv.html("(n=" + data.count_sv + ")&nbsp;");
346
- if (plot.mutation_count.fusion) plot.mutation_count.fusion.html("(n=" + data.count_fusion + ")&nbsp;");
347
- if (plot.mutation_count.itd) plot.mutation_count.itd.html("(n=" + data.count_itd + ")&nbsp;");
348
- }
349
- }).catch((e) => {
350
- obj.sayerror(e);
351
- }).then(() => {
352
- plot.button.text("Update plot").attr("disabled", null);
353
- });
354
- }
355
- function show_dividerules(p, div) {
356
- if (!p.samplerule.set) return;
357
- const st = p.samplerule.set;
358
- if (st.geneexpression) {
359
- if (!st.bymedian && !st.byquartile) {
360
- st.bymedian = 1;
361
- }
362
- const row = div.append("div").style("margin-bottom", "10px");
363
- row.append("span").style("opacity", 0.5).html("Divide samples by " + st.gene + " expression with&nbsp;");
364
- const s = row.append("select").on("change", (event) => {
365
- const o = event.target.options[event.target.selectedIndex];
366
- if (o.median) {
367
- p.samplerule.set.bymedian = 1;
368
- delete p.samplerule.set.byquartile;
369
- span_quartilecompare.style("display", "none");
370
- } else if (o.quartile) {
371
- p.samplerule.set.byquartile = 1;
372
- delete p.samplerule.set.bymedian;
373
- span_quartilecompare.style("display", "inline");
374
- }
375
- });
376
- s.append("option").text("median (group=2)").property("median", 1);
377
- s.append("option").text("quartile (group=4)").property("quartile", 1);
378
- const span_quartilecompare = row.append("span").style("margin-left", "10px");
379
- span_quartilecompare.append("span").html("Compare each quartile against&nbsp;").style("opacity", 0.5);
380
- {
381
- const s2 = span_quartilecompare.append("select").on("change", (event) => {
382
- delete p.samplerule.set.against1st;
383
- delete p.samplerule.set.against4th;
384
- switch (event.target.selectedIndex) {
385
- case 0:
386
- break;
387
- case 1:
388
- p.samplerule.set.against1st = 1;
389
- break;
390
- case 2:
391
- p.samplerule.set.against4th = 1;
392
- break;
393
- }
394
- });
395
- s2.append("option").text("none");
396
- s2.append("option").text("first quartile");
397
- s2.append("option").text("fourth quartile");
398
- if (st.against1st) {
399
- s2.node().selectedIndex = 1;
400
- } else if (s2.against4th) {
401
- s2.node().selectedIndex = 2;
402
- }
403
- }
404
- if (st.bymedian) {
405
- s.node().selectedIndex = 0;
406
- span_quartilecompare.style("display", "none");
407
- } else if (st.byquartile) {
408
- s.node().selectedIndex = 1;
409
- span_quartilecompare.style("display", "inline");
410
- }
411
- }
412
- if (st.mutation) {
413
- p.mutation_count = {};
414
- if (st.snvindel) {
415
- const row = div.append("div").style("margin-bottom", "20px");
416
- p.mutation_count.snvindel = row.append("span");
417
- if (st.snvindel.name) {
418
- row.append("span").html("SNV/indel&nbsp;");
419
- const s = row.append("select");
420
- s.append("option").text(st.snvindel.name).property("named", 1);
421
- s.append("option").text("any mutation at " + st.chr + ":" + st.start);
422
- } else {
423
- row.append("span").text("SNV/indel at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop));
424
- }
425
- }
426
- if (st.cnv) {
427
- const row = div.append("div").style("margin-bottom", "20px");
428
- p.mutation_count.cnv = row.append("span");
429
- row.append("span").html(
430
- "Copy number variation over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
431
- );
432
- }
433
- if (st.loh) {
434
- const row = div.append("div").style("margin-bottom", "20px");
435
- p.mutation_count.loh = row.append("span");
436
- row.append("span").html(
437
- "LOH over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
438
- );
439
- }
440
- if (st.sv) {
441
- const row = div.append("div").style("margin-bottom", "20px");
442
- p.mutation_count.sv = row.append("span");
443
- row.append("span").html("SV at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + "&nbsp;");
444
- }
445
- if (st.fusion) {
446
- const row = div.append("div").style("margin-bottom", "20px");
447
- p.mutation_count.fusion = row.append("span");
448
- row.append("span").html("Fusion at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + "&nbsp;");
449
- }
450
- if (st.itd) {
451
- const row = div.append("div").style("margin-bottom", "20px");
452
- p.mutation_count.itd = row.append("span");
453
- row.append("span").html(
454
- "ITD over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
455
- );
456
- }
457
- }
458
- }
459
- function show_sampleinput(p, div) {
460
- let rendered_flag = div.selectAll("div").size();
461
- if (rendered_flag) return;
462
- const row = div.append("div").style("margin-bottom", "10px");
463
- const samplelist_div = row.append("div").style("margin-left", "20px");
464
- samplelist_div.append("div").style("vertical-align", "top").style("display", "inline-block").style("opacity", 0.5).html("Enter sample names<br>(one sample per line) &nbsp;");
465
- const sample_input = samplelist_div.append("textarea").style("display", "inline-block").attr("cols", "20").attr("rows", "10").on("change", () => {
466
- let sampleset = p.samplerule.full.sampleset = [];
467
- const str = sample_input.property("value").trim();
468
- if (!str) return;
469
- for (const sample of str.split("\n")) {
470
- sampleset.push(sample);
471
- }
472
- });
473
- }
474
- export {
475
- init
476
- };
477
- //# sourceMappingURL=mds.survivalplot-77UEBQIC.js.map
@@ -1,83 +0,0 @@
1
- import {
2
- getPillNameDefault,
3
- set_hiddenvalues
4
- } from "./chunk-PC4MFDHP.js";
5
- import "./chunk-HJ6L54YS.js";
6
- import "./chunk-KV4W2ACA.js";
7
- import "./chunk-HPAW7XDM.js";
8
- import "./chunk-ELJX3QIQ.js";
9
- import "./chunk-BZN2O76M.js";
10
- import "./chunk-EEB5VE2A.js";
11
- import "./chunk-6RRZRISL.js";
12
- import "./chunk-2KM4PRQM.js";
13
- import "./chunk-52QHIKH2.js";
14
- import "./chunk-A2ORIMUJ.js";
15
- import "./chunk-PPSWNLMG.js";
16
- import "./chunk-RUBZCKIX.js";
17
- import "./chunk-WINIL2KN.js";
18
- import "./chunk-PF4DSFDR.js";
19
- import "./chunk-7X6NF7NI.js";
20
- import "./chunk-W5J3LTYS.js";
21
- import "./chunk-Z2ZITHT4.js";
22
- import "./chunk-4OLM3KSB.js";
23
- import "./chunk-FXQXCOII.js";
24
- import "./chunk-TLT4YIG3.js";
25
- import "./chunk-5R63Q5KH.js";
26
- import "./chunk-I6Y4O3RR.js";
27
- import "./chunk-Q5RDQNIT.js";
28
- import "./chunk-DQC5FFGV.js";
29
- import "./chunk-HS5PO5ZQ.js";
30
-
31
- // termsetting/handlers/multivalue.ts
32
- function getHandler(self) {
33
- return {
34
- getPillName(d) {
35
- return getPillNameDefault(self, d);
36
- },
37
- getPillStatus() {
38
- const hidden = Object.keys(self.q?.hiddenValues || {}).length;
39
- if (hidden) return { text: `${hidden} hidden` };
40
- },
41
- async showEditMenu(div) {
42
- await makeCategoryMenu(self, div);
43
- }
44
- };
45
- }
46
- async function makeCategoryMenu(self, div) {
47
- const data = await self.vocabApi.getCategories(self.term, self.filter);
48
- const lst = (data.lst || []).sort((a, b) => b.samplecount - a.samplecount);
49
- const holder = div.append("div").style("padding", "10px");
50
- if (!lst.length) {
51
- holder.append("div").style("opacity", 0.6).text("No categories");
52
- return;
53
- }
54
- holder.append("div").style("opacity", 0.6).style("font-size", ".8em").style("padding-bottom", "5px").text("CHECK TO SHOW CATEGORY");
55
- const checkboxes = /* @__PURE__ */ new Map();
56
- for (const c of lst) {
57
- const row = holder.append("div");
58
- const label = row.append("label");
59
- const checkbox = label.append("input").attr("type", "checkbox").property("checked", !self.q.hiddenValues?.[c.key]);
60
- checkboxes.set(c.key, checkbox);
61
- label.append("span").text(` ${c.label || c.key} `);
62
- label.append("span").style("opacity", 0.6).style("font-size", ".8em").text(`n=${c.samplecount}`);
63
- }
64
- holder.append("button").style("margin-top", "10px").text("Apply").on("click", () => {
65
- const hiddenValues = {};
66
- for (const [key, checkbox] of checkboxes) {
67
- if (!checkbox.property("checked")) hiddenValues[key] = 1;
68
- }
69
- self.q.hiddenValues = hiddenValues;
70
- self.dom.tip.hide();
71
- self.api.runCallback();
72
- });
73
- }
74
- function fillTW(tw, _vocabApi) {
75
- const q = tw.q;
76
- if (!q.type) q.type = "values";
77
- set_hiddenvalues(q, tw.term);
78
- }
79
- export {
80
- fillTW,
81
- getHandler
82
- };
83
- //# sourceMappingURL=multivalue-KZ2DMVIR.js.map
@@ -1,63 +0,0 @@
1
- import {
2
- NumericModes
3
- } from "./chunk-PPSWNLMG.js";
4
- import "./chunk-RUBZCKIX.js";
5
- import "./chunk-Z2ZITHT4.js";
6
- import "./chunk-4OLM3KSB.js";
7
- import "./chunk-5R63Q5KH.js";
8
- import "./chunk-I6Y4O3RR.js";
9
- import "./chunk-Q5RDQNIT.js";
10
- import "./chunk-HS5PO5ZQ.js";
11
-
12
- // plots/numericDictTermCluster.ts
13
- function makeChartBtnMenu(holder, chartsInstance) {
14
- chartsInstance.dom.tip.clear();
15
- const menuDiv = holder.append("div");
16
- const numericDictTermCluster = chartsInstance.state.termdbConfig.numericDictTermCluster;
17
- if (numericDictTermCluster?.plots) {
18
- for (const plot of numericDictTermCluster.plots) {
19
- menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
20
- chartsInstance.dom.tip.hide();
21
- const config = await chartsInstance.app.vocabApi.getNumericDictTermClusterByName(plot.name);
22
- config.preBuiltPlotTitle = plot.name;
23
- chartsInstance.app.dispatch({
24
- type: "plot_create",
25
- config
26
- });
27
- });
28
- }
29
- }
30
- const chart = {
31
- //use the app name defined in dataset file
32
- label: numericDictTermCluster?.appName || "Numeric Dictionary Term cluster",
33
- chartType: "numericDictTermCluster",
34
- clickTo: chartsInstance.showTree_selectlst,
35
- minTermsToSubmit: 3,
36
- usecase: {
37
- target: "numericDictTermCluster",
38
- detail: { exclude: numericDictTermCluster?.exclude }
39
- },
40
- updateActionBySelectedTerms: (action, termlst) => {
41
- if (!termlst?.length) throw "cannot launch clustering: no terms selected";
42
- const twlst = termlst.map((term) => ({
43
- term: structuredClone(term),
44
- q: { mode: NumericModes.continuous }
45
- }));
46
- action.config.chartType = "hierCluster";
47
- action.config.dataType = twlst[0].term.type || "float";
48
- if (numericDictTermCluster?.appName) action.config.appName = numericDictTermCluster.appName;
49
- action.config.termgroups = [
50
- {
51
- name: numericDictTermCluster?.settings?.termGroupName || "Numeric Dictionary Term Cluster",
52
- lst: twlst,
53
- type: "hierCluster"
54
- }
55
- ];
56
- }
57
- };
58
- chartsInstance.showTree_selectlst(chart);
59
- }
60
- export {
61
- makeChartBtnMenu
62
- };
63
- //# sourceMappingURL=numericDictTermCluster-C2MYJYPZ.js.map